ELIXIR-CONVERGE D8.5 Data access points and tools

Within the scope of deliverable 8.5 which was to enhance access to the COVID-19 Data Portal data, we developed the following data access support tools and services:

COVID-19 Data Portal API: a proxy layer on top of EBI search pulling together a diverse range of resources into a single search service.

COVID-19 Data Portal Download: an interactive download tool, allowing users to select different formats for metadata and data downloads.

OmicsDI Indexing Service: an integrated and open source platform which indexes sources external to EBI and enables display on the COVID-19 Data Portal. Two ELIXIR core resources have been indexed: Cellosaurus and HPA.

Covid-19 Data Portal File Downloader Tool: a user runnable tool for downloading all host and viral sequence data from ENA (European Nucleotide Archive) as seen on the COVID-19 Data Portal. The tool can download data in different formats and can generate scripts that run interactively with local data syncing of COVID-19 data available on the Portal.

Third-Party Tools: Open data sharing has led to the further development of additional open-source tools that provide support to the wider scientific community. As part of the COVID-19 Data Platform three main examples of such tools have been identified: the COVID-19 Viral Beacon, Nextrain's public phylogeny and report for INSDC-submitted consensus sequences, and Galaxy.

GISAID Metadata Conversion Tool: to support users who have been sharing data with GISAID, this tool converts a metadata spreadsheet used during the GISAID submission process, to a sample XML file that is compatible with ENA’s programmatic submission process.